[Objective] To isolate and characterize ocular Chlamydia trachomatis from trachoma samples of Tibetan children from Qinghai province. [Methods] Swabs of left and right conjunctivas and conjunctival sacs were collected into one milliliter of transportation media. Fifty microliters of each sample were used to infect BGM cells by using centrifugation. Infected cells were cultured at 37 °C for 72 h, and were passaged for three successive times. Chlamydial inclusions were observed using phase microscopy. Chlamydial cultures and clinical samples were characterized by using ompA gene sequence analyses. [Results] A total of 115 samples from 45 trachoma patients were collected. 54 samples were ompA-PCR positive and 15 samples were culture positive. All ompA genes of these samples belong to genotype B, are grouped into 3 variants and have a UGT-type codon. Chlamydial isolates QH111L and QH111R were from left and right conjunctival samples of No. 111 patient, respectively, but their ompA genes have a nonsynonymous base difference. This single nucleotide change was only found in left conjunctiva of No. 111 patient, suggesting that QH111L may be a newly emerged ompA variant. [Conclusion] 15 ocular Chlamydia trachomatis strains were isolated from Tibetan children of Qinghai. All strains belong to genotype B and three different ompA variants. Isolates from a same patient’s separate conjunctivas were found to have different ompA genes. Identification and characterization of these newly isolated strains will further our understanding of trachoma epidemiology and evolution.